Confused on Paths

So do templates use one path, and the modules use another? This is running on a 5. core.

So what should the path be? I believe the proper setting to be
files/example.com

Here's what it looks like on the server:

/home/drupal/files/example.com/ drwxrwxr-x 4 apache apache 4.0K Mar 6 18:17

Those are same same. Exactly as I'd expect them to be.

I have the site web root set like so in Apache
/home/user/sites/example.com/html

So what's in those dirs
lrwxrwxrwx 1 root root 36 Mar 6 17:57 files -> /home/drupal/files/example.com/

I've tried this several different ways e.g. rm file and then ln -s /home/drupal/files/ files
One step forward, one back. Bueditor is there now, but all the other files have broken since they're back in files/example.com
If I drop the files in /home/drupal/files it'll work, but I don't want every site's files in /home/drupal/files they should be in /home/drupal/files/example.com

I hope that made sense. So the home dir is here
/home/user/sites/example.com/html

If in there I have the files dir set a link here:
/home/drupal/files/example.com/ files
The theme works, but bueditor doesn't
If in there I have the files dir set a link here:
/home/drupal/files/
The buedior works, but the theme isn't getting the right path.